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| Status |
Public on Sep 08, 2016 |
| Title |
AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Alternative splicing of pre-mRNAs significantly contributes to the complexity of gene expression in higher organisms, but the regulation of the splice site selection remains incompletely understood. We have previously demonstrated that a chromatin-associated protein, AKAP95 (AKAP8), has a remarkable activity in enhancing chromatin transcription. In this study, we have shown that AKAP95 physically interacts with many factors involved in transcription and RNA processing, and functionally regulates pre-mRNA splicing. AKAP95 directly promotes splicing in vitro and the inclusion of a specific exon of an endogenous gene FAM126A. The N-terminal YG-rich domain of AKAP95 is important for its binding to RNA processing factors including selective groups of hnRNP proteins, and its zinc finger domains are critical for pre-mRNA binding. Genome-wide binding assays revealed that AKAP95 bound preferentially to proximal intronic regions on a large number of pre-mRNAs in human transcriptome, and AKAP95 depletion predominantly resulted in reduced inclusion of many exons. AKAP95 also selectively coordinates with hnRNP H/F and U proteins in regulating alternative splicing events. We have further shown that AKAP95 directly interacts with itself. Taken together, our results establish AKAP95 as a novel and mostly positive regulator of pre-mRNA splicing and a possible integrator of transcription and splicing regulation, and support a model that AKAP95 regulates pre-mRNA splicing via through scaffolding RNAs and RNA processing factors and facilitating the splice site communication.
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| Overall design |
Samples 1-8 are RNA-immunoprecipitation (RIP)-seq to determine AKAP95 binding to the transcriptome. Samples 9-15 are mRNA-seq to determine effect of AKAP95 knockdown in human 293 cells (9-11) or mouse ES cells (12-15).
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| Contributor(s) |
Khodadadi-Jamayran A, Hu J, Jiang H |
| Citation(s) |
27824034 |
| |
| Submission date |
May 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alireza Khodadadi-Jamayran |
| Organization name |
New York University, NYU Langone Medical Center
|
| Department |
Division of Advanced Research Technologies (DART)
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| Lab |
Applied Bioinformatics Laboratories (ABL)
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| Street address |
550 1st Ave, MSB 304
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| City |
New York City |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA323422 |
| SRA |
SRP075747 |
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